GNB4

protein-coding

G protein subunit beta 4, the group of G protein subunits beta|WD repeat domain containing

Gene summary

Heterotrimeric guanine nucleotide-binding proteins (G proteins), which integrate signals between receptors and effector proteins, are composed of an alpha, a beta, and a gamma subunit. These subunits are encoded by families of related genes. This gene encodes a beta subunit. Beta subunits are important regulators of alpha subunits, as well as of certain signal transduction receptors and effectors. [provided by RefSeq, Jul 2008]

MANE transcript

NM_021629.4

Inheritance

AD

ClinVar variants

P:6U:138B:80

Top phenotype

Charcot-Marie-Tooth disease, dominant intermediate F

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr3:179,396,088-179,451,476

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~55.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Charcot-Marie-Tooth diseaseMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0015626

Submitter: ClinGen

GNB4 was first reported in relation to autosomal dominant Charcot-Marie-Tooth Disease in 2013 (Soong et al., PMID: 23434417). Reported cases to date have an adolescent onset and are further characterized by slowly progressive distal muscle atrophy and weakness, distal sensory impairment with decreased reflexes, and variable nerve conduction velocities ranging from the demyelinating to the axonal range. Four missense variants, two of which are de novo, have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. Variants in this gene have been reported in at least four probands in three separate publications (PMIDs: 23134117, 28642160, 27908631). Variants in this gene segregated with disease in five additional family members in one large family. Although the initial characterization evidence to support pathogenicity, there is a lack of appropriate supporting evidence for the latter two cases. This gene-disease relationship is additionally supported by expression data and functional alteration of human oligodendrocyte progenitor cells (hOPCs). Investigation determined that GNB4 is largely expressed in axons and Schwann cells of neurons, relating to the neurodegenerative phenotypes characteristic of CMT. Additionally, mice with an immunodeficient, demyelinating phenotype were injected with hOPCs both expressing and not expressing GNB4 and found a large increase in the latter's differentiation compared to the controls, suggesting a major role in myelin development and differentiation. Although there is additional evidence available, the lack of the exact mechanism and an animal model limits the scorable data. In summary, there is MODERATE evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Charcot-Marie-Tooth Expert Panel on 02/25/20 (SOP Version 007). **Recuration update**: Four additional unrelated families from two publications were curated, providing new genetic evidence supporting the association between GNB4 and autosomal dominant Charcot-Marie-Tooth disease. Kwon et al. (2021; PMID: 34071515) reported three unrelated Korean families carrying heterozygous GNB4 variants. One family harbored the novel c.229G>A (p.Gly77Arg) variant, which occurred de novo in a patient with intermediate CMT and was absent from both unaffected parents. Although no variant-specific functional studies were performed, the phenotype was highly consistent with GNB4-associated neuropathy, and the variant affected a highly conserved residue within the WD40 repeat domain. This proband was scored as 1.0 point. Two additional unrelated families carried the recurrent c.265A>G (p.Lys89Glu) variant, each arising independently as a de novo event. This variant had previously been established as pathogenic and was supported by published functional studies demonstrating impaired GPCR signaling. Given the independent de novo occurrences of a recurrent pathogenic variant and the highly specific neuropathy phenotype, each family was scored as 1.5 points, contributing a total of 4.0 genetic evidence points. Pretkalnina et al. (2025; PMID: 41164122) described an additional unrelated autosomal dominant family carrying the novel c.239T>C (p.Ile80Thr) variant. The variant segregated with disease in multiple affected family members and was supported by extensive variant-specific functional studies demonstrating reduced Gβ4 protein expression, abnormal intracellular localization, and impaired GPCR signaling with significantly reduced IP₁ production. Based on the segregation data, highly consistent phenotype, and strong functional evidence, this family was scored as 1.0 point. Together, these publications contributed five additional genetic evidence points, increasing the total genetic evidence score further strengthening the association between GNB4 and autosomal dominant CMT. The total evidence reached 10.6 points which is still equivalent to Moderate classification, although the evidence remains just below the threshold for a definitive classification

Charcot-Marie-Tooth disease dominant intermediate FSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014074

Submitter: PanelApp Australia

Charcot-Marie-Tooth disease dominant intermediate FSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014074

Submitter: Orphanet

Charcot-Marie-Tooth disease dominant intermediate FSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014074

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Charcot-Marie-Tooth disease, dominant intermediate FAD

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 20627571; 23434117Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GNB4 variants in ClinVar

7 Conditions Cataloged
Charcot-Marie-Tooth disease dominant intermediate FTotal: 249
Inborn genetic diseasesTotal: 51
not providedTotal: 50
GNB4-related disorderTotal: 24
not specifiedTotal: 21
See casesTotal: 2
Charcot-Marie-Tooth diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021629.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
6
clinvar
63
clinvar
69
missense
2
clinvar
4
clinvar
112
clinvar
17
clinvar
135
nonsense
7
clinvar
7
start loss
0
frameshift
6
clinvar
6
splice donor/acceptor (+/-2bp)
7
clinvar
7
Total24138800224

Highest pathogenic variant AF is 0.000004956218

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_021629.4RefSeqNP_067642.19MANE Select
ENST00000232564.8EnsemblENSP00000232564.39MANE Select
ENST00000465153.2EnsemblENSP00000502010.18Standard
ENST00000466899.6EnsemblENSP00000420066.28Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Relaxin signaling pathway - Homo sapiens (human)
  • Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
  • Retrograde endocannabinoid signaling - Homo sapiens (human)
  • GABAergic synapse - Homo sapiens (human)

Biological Process

  • protein folding
  • signal transduction
  • substantia nigra development

Molecular Function

  • protein-containing complex binding

Cellular Component

  • lysosomal membrane
  • cytosol
  • myelin sheath
  • extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000232564
Coding exons
9
Length
52389
Individuals with no LoFs
125732
Homozygous LoFs
0
Heterozygous LoFs
16
Defined
125748
p
0.0000636
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.111121950.5750.00001062228
Missense (PolyPhen)2767.4630.40022788
Synonymous0.6966067.30.8920.00000357645
Loss of Function2.58820.70.3870.00000118221

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.0000560.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000790.000079rare
South Asian0.000100.000098rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein- effector interaction.;

Recessive Scores

pRec
0.130

Intolerance Scores

LoFtool
0.614
RVIS EVS
-0.03
RVIS percentile EVS
51.4

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.915

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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